Hello, welcome to the community! And thank you for asking.
I would recommend creating a multi-root workspace.
You can start with your current project-A folder open, then use File > Add Folder to Workspace... to add project-B as a separate workspace folder.
You can then use File > Save Workspace As... to save this workspace layout and have it automatically reopened the next time you start the IDE.
This way, each workspace folder is seen by the IDE as a separate configuration scope, and each can be bound to a different project on SQ:Cloud.